[med-svn] r6744 - in trunk/packages/amap-align/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2011-05-02 14:40:01 +0000 (Mon, 02 May 2011)
New Revision: 6744

Added:
   trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.6.diff
Modified:
   trunk/packages/amap-align/trunk/debian/changelog
   trunk/packages/amap-align/trunk/debian/compat
   trunk/packages/amap-align/trunk/debian/control
   trunk/packages/amap-align/trunk/debian/patches/series
Log:
Fix gcc-4.6 build error


Modified: trunk/packages/amap-align/trunk/debian/changelog
===================================================================
--- trunk/packages/amap-align/trunk/debian/changelog	2011-05-02 14:26:40 UTC (rev 6743)
+++ trunk/packages/amap-align/trunk/debian/changelog	2011-05-02 14:40:01 UTC (rev 6744)
@@ -1,3 +1,12 @@
+amap-align (2.2-3) unstable; urgency=low
+
+  * Standards-Version: 3.9.2 (no changes needed)
+  * Debhelper 8 (compat+control)
+  * debian/patches/fix-gcc-4.6.diff: Fix gcc-4.6 build error
+    Closes: #624990
+
+ -- Andreas Tille <tille at debian.org>  Mon, 02 May 2011 16:30:17 +0200
+
 amap-align (2.2-2) unstable; urgency=low
 
   [ Charles Plessy ]

Modified: trunk/packages/amap-align/trunk/debian/compat
===================================================================
--- trunk/packages/amap-align/trunk/debian/compat	2011-05-02 14:26:40 UTC (rev 6743)
+++ trunk/packages/amap-align/trunk/debian/compat	2011-05-02 14:40:01 UTC (rev 6744)
@@ -1 +1 @@
-7
+8

Modified: trunk/packages/amap-align/trunk/debian/control
===================================================================
--- trunk/packages/amap-align/trunk/debian/control	2011-05-02 14:26:40 UTC (rev 6743)
+++ trunk/packages/amap-align/trunk/debian/control	2011-05-02 14:40:01 UTC (rev 6744)
@@ -5,8 +5,8 @@
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>,
  Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7), quilt
-Standards-Version: 3.9.1
+Build-Depends: debhelper (>= 8), quilt
+Standards-Version: 3.9.2
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/amap-align/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/amap-align/trunk/
 X-Homepage: http://bio.math.berkeley.edu/amap/ - upstream seems to be dead
@@ -18,8 +18,8 @@
 Description: Protein multiple alignment by sequence annealing
  AMAP is a command line tool to perform multiple alignment of peptidic
  sequences. It utilizes posterior decoding, and a sequence-annealing
- alignment, instead of the traditional progressive alignment method. It
- is the only alignment program that allows to control the sensitivity /
+ alignment, instead of the traditional progressive alignment method. It is
+ the only alignment program that allows one to control the sensitivity /
  specificity tradeoff.  It is based on the ProbCons source code, but
  uses alignment metric accuracy and eliminates the consistency
  transformation.

Added: trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.6.diff
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.6.diff	                        (rev 0)
+++ trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.6.diff	2011-05-02 14:40:01 UTC (rev 6744)
@@ -0,0 +1,10 @@
+--- amap-align-2.2.orig/align/SafeVector.h
++++ amap-align-2.2/align/SafeVector.h
+@@ -10,6 +10,7 @@
+ 
+ #include <cassert>
+ #include <vector>
++#include <cstddef>
+ 
+ /////////////////////////////////////////////////////////////////
+ // SafeVector

Modified: trunk/packages/amap-align/trunk/debian/patches/series
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/series	2011-05-02 14:26:40 UTC (rev 6743)
+++ trunk/packages/amap-align/trunk/debian/patches/series	2011-05-02 14:40:01 UTC (rev 6744)
@@ -1 +1,2 @@
 fix-gcc-4.3.diff
+fix-gcc-4.6.diff